Merge pull request #223 from jfennick/compute_remove_temporarily

temporarily remove legacy Labshare Compute API

docs/dev/api.rst

@@ -29,10 +29,6 @@ wic.input_output
 ------------------------------------
 .. automodule:: wic.input_output
 
-wic.labshare
-------------------------------------
-.. automodule:: wic.labshare
-
 wic.main
 ------------------------------------
 .. automodule:: wic.main

docs/index.rst

@@ -10,7 +10,6 @@ Workflow Inference Compiler documentation
    tutorials/tutorials.rst
    userguide.md
    advanced.md
-   compute.md
    validation.md
    dev/installguide.md
    dev/devguide.md

src/wic/cli.py

@@ -69,17 +69,9 @@
                        help='Just generates run.sh and exits. Does not actually invoke ./run.sh')
 group_run.add_argument('--run_local', default=False, action="store_true",
                        help='After generating the cwl file(s), run it on your local machine.')
-group_run.add_argument('--run_compute', default=False, action="store_true",
-                       help='After generating the cwl file(s), run it on the remote labshare Compute platform.')
-parser.add_argument('--compute_driver', type=str, required=False, default='slurm', choices=['slurm', 'argo'],
-                    help='The driver to use for running workflows on labshare Compute.')
-# Use required=('--run_compute' in sys.argv) make other args conditionally required.
-# See https://stackoverflow.com/questions/19414060/argparse-required-argument-y-if-x-is-present
-# For example, if run_compute is enabled, you MUST enable cwl_inline_subworkflows!
-# Plugins with 'class: Workflow' (i.e. subworkflows) are not currently supported.
 
-parser.add_argument('--cwl_inline_subworkflows', default=('--run_compute' in sys.argv), action="store_true",
-                    help='Before generating the cwl file, inline all subworkflows. Required for --run_compute')
+parser.add_argument('--cwl_inline_subworkflows', default=False, action="store_true",
+                    help='Before generating the cwl file, inline all subworkflows.')
 parser.add_argument('--inference_disable', default=False, action="store_true",
                     help='Disables use of the inference algorithm when compiling.')
 parser.add_argument('--inference_use_naming_conventions', default=False, action="store_true",
@@ -95,15 +87,6 @@
 parser.add_argument('--cachedir', type=str, required=False, default='cachedir',
                     help='The directory to save intermediate results; useful with RealtimePlots.py')
 
-AWS_URL = 'http://compute.ci.aws.labshare.org'
-NCATS_URL = 'https://compute.scb-ncats.io/'
-
-parser.add_argument('--compute_url', type=str, default=NCATS_URL,
-                    help='The URL associated with the labshare Compute API. Required for --run_compute')
-parser.add_argument('--compute_access_token', type=str, required=('--run_compute' in sys.argv),
-                    help="""The access_token used for authentication. Required for --run_compute
-                    For now, get this manually from https://a-qa.labshare.org/""")
-
 parser.add_argument('--graphviz', default=False, action="store_true",
                     help='Generate a DAG using graphviz.')
 parser.add_argument('--graph_label_edges', default=False, action="store_true",

src/wic/main.py

@@ -11,7 +11,7 @@
 
 from wic.utils_yaml import wic_loader
 from . import input_output as io
-from . import ast, cli, compiler, inference, inlineing, labshare, plugins, run_local, utils  # , utils_graphs
+from . import ast, cli, compiler, inference, inlineing, plugins, run_local, utils  # , utils_graphs
 from .schemas import wic_schema
 from .wic_types import GraphData, GraphReps, Json, StepId, Yaml, YamlTree
 
@@ -161,14 +161,6 @@ def main() -> None:
         rose_tree = plugins.cwl_update_outputs_optional_rosetree(rose_tree)
         io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
 
-    if args.run_compute:
-        # Inline compiled CWL if necessary, i.e. inline across scattering boundaries.
-        # NOTE: Since we need to distribute scattering operations across all dependencies,
-        # and due to inference, this cannot be done before compilation.
-        rose_tree = inlineing.inline_subworkflow_cwl(rose_tree)
-        io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
-        labshare.upload_all(rose_tree, tools_cwl, args, True)
-
     if args.graphviz:
         if shutil.which('dot'):
             # Render the GraphViz diagram